I have reproduced and investigated this problem on Windows. The problem is the Segoe UI font, which the default PixInsight style sheet uses on all supported versions of Windows. Unfortunately, the numerals in this font are rendered with a strange left displacement, something like a negative kerning, which causes this two-pixel clipping. This might be a Qt font rendering problem. There's no way to fix this with CSS code, since it has nothing to do with margin properties, and the clipping occurs 'behind' the left padding, so changing the padding only moves the text but doesn't fix the clipping.
I am considering using a different font for the Windows versions of PixInsight. A good candidate would be Verdana. Another possibility, probably more robust, would be including a custom font in the PixInsight distribution, just as we have now Deja Vu Sans on all platforms. Unfortunately, Deja Vu has some rendering problems on Windows that make it a poor choice for the whole GUI.
In the meanwhile, I think that adding a space at the beginning of each combo box item is the best solution. Note that this is only necessary if the combo box items start with a decimal digit character.
